Zotfile does not extract highlights

I recently installed Zotfile, after which I tested it with a PDF file that had a few highlights. The extraction worked well.
I now have a PDF with some 140 pages, and more highlights, though certainly not on every page, but the extraction does not work. The notification box telling me that the extraction is taking place stays there but there is no result
Any suggestions?
  • Is there a maximum that Zotero can handle?
  • Definitely not a Zotero problem, but it's certainly conceivable that ZotFile might get stuck.

    You've annotated the PDF with the same software you used in tests?
  • @adamsmith: what makes you so sure it is definitely not a Zotero problem?
    As for the annotation software, I think it was the same, but am not 100% sure. I only use highlights. If I understand you well, though, Zotero/Zotfile can only handle annotations from certain software and not from others. If that's correct, then is there a list of acceptable software?
  • It's not Zotero because the only part of Zotero involved is the ability to create notes for ZotFile and that either works or it doesn't.

    ZotFile is able to extract standard annotations on PDF. Most tools use standard annotations, but some don't. There's no list of tools, no. A rule of thumb is, if you can see the annotations when viewing the annotated PDF in Firefox, ZotFile should be able to extract them.
  • @adamsmith well, using your rule of thumb Zotfile should be able to extract them because the highlights are in bright yellow.
  • @adamsmith so if I understand well Zotero is not able to extract certain highlights. Would it help if those highlights were in green instead of yellow?
  • The highlight color is irrelevant.
  • edited April 4, 2019
    @DWL-SDCA thanks for your reply. So, if the highlight colour is irrelevant, how come Zotero is not extracting, as I described in the beginning?
    @adamsmith makes a point of the software used. Now, I am not a Zotero expert, but it seems strange that Zotero would only extract highlights done with certain software. This is even stranger considering there is not approved software list.
  • There may be a misunderstanding. Zotero does not extract highlights. That is done by ZotFile, a third-party plugin that is not maintained by Zotero.

    Although ZotFile is useful and popular, as far as I know it is not being actively maintained beyond perhaps basic bug fixes. The people here can help identify what works with it and what doesn't and why, but I don't think anyone is in a position to provide bespoke extensions to its current functionality.
  • @fbennett thanks for clearing that up.
  • I apologize for not being more clear. I was writing about ZotFile not caring about highlight color. If someone doesn't ninja me, I'll try to comment soon on several pdf annotation programs that work with Zotfile.
  • Sure, a list is fine, but the basic rule is that ZotFile will recognize annotations according the the PDF standard and won't recognize annotations that don't follow the standard (it uses the same tool to recognize them that Firefox uses to display PDFs. That's why the above rule of thumb, btw.). That means the majority of pdf readers/annotators are supported. Probably the most notable tool ZotFile doesn't work with is Skim for Mac, but there are others.*

    It does sound like, though, that the problem may well be something different than the tool used for annotating. Simplest way to tell would be for @KlaasVaak to use the same method on a very simple document. If extraction works there, the problem is elsewhere. Could be a problem with the document, e.g. document security properties that prevent copying text, or could be a ZotFile bug, e.g. related to the long document. I'd do this simple troubleshooting before spending a lot of time thinking about supported and not supported annotation tools. If you're using a common tool for annotating, you could also just tell us and we'll likely know.


    * There is one other slight quirk to this in that ZotFile doesn't recognize all _types_ of annotations. It does recognize standard highlighting (indeed, regardless of color) and it recognizes standard comments, but e.g. I don't think it recognizes text that you associate with highlighting, nor does it recognize other textbox formats you can generate in some tools including Acrobat.
  • What I think I may have done is to do the test annotations in Foxit Reader. Then, when I went on to annotate my 140 page PDF, I used Okular.
    @adamsmith can you tell me what the Zotfile support status for these 2 programs is?
  • edited April 5, 2019
    @KlaasVaak One thing to try, if you haven't already, is to print the Okular-annotated file to PDF. That will change its internal structure, and possibly (although only possibly) put the annotations into a form that ZotFile can extract. I've seen that work with Okular files in other contexts, it's worth a try.
  • Yes, what fbennett says exactly. Okular _can_ write extractable annotations, but I don't think they are by default. FoxIt definitely works.
  • @fbennett unfortunately that did not work. As soon as I set Zotfile to extract the annotations from the secondary PDF file, the rectangular Zotfile pop-up in the bottom right corner showed the name of the file with a red cross before it, nothing at all was extracted.

    I then tried an older file with 200 pages that I knew for sure I had annotated in Foxit, and that worked. Ironically, the Windows version of Foxit has its built-in annotations export feature, but not in the Linux version :-(((

    So, the take away for me is that I should not use Okular anymore (I always apply annotations to PDFs) and reinstall Foxit, which I had installed and uninstalled because of the lack of this feature. Zotfile has "saved" me :-)

    A big thanks to you and @adamsmith for your help, as well as your time.
  • For reference, Okular has changed behaviour with how they write annotations multiple times since adding support, so it's hard to always say what it will do for individual users. Linux distributions with long support cycles may still include versions that are several years old.

    The version I have here prompts (with a permanently dismissable alert) when I add an annotation, that I need to "File -> Save As..." to preserve the annotations, which writes them to the file in a way ZotFile can read. For Zotero/ZotFile to be aware of it, you must overwrite the same file that is already there.

    I'll also note that ZotFile does not extract an "Inline Note" but does extract highlighted text, and text from a "Pop-up Note"
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